Multiple platform build/check report for BioC 3.24 - CHECK results for SIAMCAT on nebbiolo2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.4 LTS)	x86_64	4.6.0 RC (2026-04-17 r89917) -- "Because it was There"	4878
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4663
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

CHECK results for SIAMCAT on nebbiolo2

To the developers/maintainers of the SIAMCAT package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SIAMCAT.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: SIAMCAT

Version: 2.17.0

Command: /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD check --install=check:SIAMCAT.install-out.txt --library=/home/biocbuild/bbs-3.24-bioc/R/site-library --timings SIAMCAT_2.17.0.tar.gz

StartedAt: 2026-05-06 04:20:22 -0400 (Wed, 06 May 2026)

EndedAt: 2026-05-06 04:31:16 -0400 (Wed, 06 May 2026)

EllapsedTime: 654.6 seconds

RetCode: 1

Status: ERROR

CheckDir: SIAMCAT.Rcheck

Warnings: NA

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD check --install=check:SIAMCAT.install-out.txt --library=/home/biocbuild/bbs-3.24-bioc/R/site-library --timings SIAMCAT_2.17.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.24-bioc/meat/SIAMCAT.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-05-06 08:20:23 UTC
* checking for file ‘SIAMCAT/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SIAMCAT’ version ‘2.17.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘SIAMCAT’ can be installed ... OK
* checking installed package size ... INFO
  installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   2.1Mb
    help      1.9Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  check.associations.Rd: lmerTest
  summarize.features.Rd: phyloseq
  train.model.Rd: mlr3learners, glmnet, LiblineaR
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                            user system elapsed
make.predictions          24.664  0.202  24.867
model.interpretation.plot 24.519  0.168  24.687
assign-model_list         24.105  0.409  24.516
train.model               22.416  0.175  22.592
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘SIAMCAT_confounder.Rmd’ using rmarkdown
The magick package is required to crop "/home/biocbuild/bbs-3.24-bioc/meat/SIAMCAT.Rcheck/vign_test/SIAMCAT/vignettes/SIAMCAT_confounder_files/figure-html/conf_assoc_plot-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.24-bioc/meat/SIAMCAT.Rcheck/vign_test/SIAMCAT/vignettes/SIAMCAT_confounder_files/figure-html/dorea_plot-1.png" but not available.
--- finished re-building ‘SIAMCAT_confounder.Rmd’

--- re-building ‘SIAMCAT_holdout.Rmd’ using rmarkdown

Quitting from SIAMCAT_holdout.Rmd:54-69 [siamcat_fr]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `file()`:
! cannot open the connection to 'https://zenodo.org/api/files/d81e429c-870f-44e0-a44a-2a4aa541b6c1/meta_Zeller.tsv'
---
Backtrace:
    ▆
 1. └─utils::read.table(...)
 2.   └─base::file(file, "rt")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'SIAMCAT_holdout.Rmd' failed with diagnostics:
cannot open the connection to 'https://zenodo.org/api/files/d81e429c-870f-44e0-a44a-2a4aa541b6c1/meta_Zeller.tsv'
--- failed re-building ‘SIAMCAT_holdout.Rmd’

--- re-building ‘SIAMCAT_meta.Rmd’ using rmarkdown

Quitting from SIAMCAT_meta.Rmd:48-62 [load_data]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! cannot open the connection
---
Backtrace:
    ▆
 1. ├─readr::read_tsv(paste0(data.loc, "meta_all_cd.tsv"))
 2. │ └─vroom::vroom(...)
 3. │   └─vroom:::vroom_(...)
 4. └─vroom (local) `<fn>`(`<curl>`, "rb")
 5.   └─base::tryCatch(...)
 6.     └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 7.       └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 8.         └─value[[3L]](cond)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'SIAMCAT_meta.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘SIAMCAT_meta.Rmd’

--- re-building ‘SIAMCAT_ml_pitfalls.Rmd’ using rmarkdown
The magick package is required to crop "/home/biocbuild/bbs-3.24-bioc/meat/SIAMCAT.Rcheck/vign_test/SIAMCAT/vignettes/SIAMCAT_ml_pitfalls_files/figure-html/plot_auroc-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.24-bioc/meat/SIAMCAT.Rcheck/vign_test/SIAMCAT/vignettes/SIAMCAT_ml_pitfalls_files/figure-html/hmp_samples-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.24-bioc/meat/SIAMCAT.Rcheck/vign_test/SIAMCAT/vignettes/SIAMCAT_ml_pitfalls_files/figure-html/plot_results_db-1.png" but not available.
--- finished re-building ‘SIAMCAT_ml_pitfalls.Rmd’

--- re-building ‘SIAMCAT_read-in.Rmd’ using rmarkdown
--- finished re-building ‘SIAMCAT_read-in.Rmd’

--- re-building ‘SIAMCAT_vignette.Rmd’ using rmarkdown
--- finished re-building ‘SIAMCAT_vignette.Rmd’

SUMMARY: processing the following files failed:
  ‘SIAMCAT_holdout.Rmd’ ‘SIAMCAT_meta.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.24-bioc/meat/SIAMCAT.Rcheck/00check.log’
for details.

Installation output

SIAMCAT.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD INSTALL SIAMCAT
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.24-bioc/R/site-library’
* installing *source* package ‘SIAMCAT’ ...
** this is package ‘SIAMCAT’ version ‘2.17.0’
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (SIAMCAT)

Tests output

Example timings

SIAMCAT.Rcheck/SIAMCAT-Ex.timings

name	user	system	elapsed
accessSlot	0.006	0.002	0.007
add.meta.pred	0.025	0.000	0.026
assign-associations	0.006	0.001	0.006
assign-data_split	0.006	0.001	0.006
assign-eval_data	0.023	0.000	0.022
assign-filt_feat	0.006	0.000	0.006
assign-label	0.005	0.000	0.005
assign-meta	0.026	0.000	0.026
assign-model_list	24.105	0.409	24.516
assign-norm_feat	0.005	0.001	0.006
assign-orig_feat	0.01	0.00	0.01
assign-physeq	0.005	0.001	0.006
assign-pred_matrix	0.007	0.000	0.007
assoc_param-methods	0.004	0.001	0.005
association.plot	0.206	0.007	0.213
associations-methods	0.005	0.002	0.008
check.associations	0.008	0.001	0.009
check.confounders	0.410	0.005	0.415
create.data.split	0.041	0.000	0.041
create.label	0.002	0.000	0.002
data_split-methods	0.005	0.000	0.004
eval_data-methods	0.005	0.000	0.005
evaluate.predictions	1.735	0.000	1.734
feature_type-methods	0.004	0.001	0.005
feature_weights-methods	0.004	0.000	0.005
filt_feat-methods	0.004	0.000	0.005
filt_params-methods	0.004	0.000	0.005
filter.features	0.013	0.000	0.013
filter.label	0.006	0.000	0.006
get.filt_feat.matrix	0.003	0.001	0.004
get.norm_feat.matrix	0.005	0.000	0.004
get.orig_feat.matrix	0.005	0.000	0.004
label-methods	0.004	0.001	0.005
make.predictions	24.664	0.202	24.867
meta-methods	0.021	0.000	0.021
model.evaluation.plot	0.022	0.003	0.025
model.interpretation.plot	24.519	0.168	24.687
model_list-methods	0.005	0.000	0.005
model_type-methods	0.004	0.001	0.005
models-methods	0.004	0.001	0.005
norm_feat-methods	0.004	0.001	0.004
norm_params-methods	0.015	0.001	0.015
normalize.features	0.017	0.001	0.018
orig_feat-methods	0.005	0.000	0.006
physeq-methods	0.01	0.00	0.01
pred_matrix-methods	0.005	0.000	0.006
read.label	0.008	0.000	0.008
read.lefse	1.182	0.074	1.256
select.samples	0.052	0.000	0.052
siamcat	0.221	0.006	0.226
siamcat.to.lefse	0.016	0.000	0.016
siamcat.to.maaslin	0.016	0.001	0.017
summarize.features	1.622	0.016	1.639
train.model	22.416	0.175	22.592
validate.data	0.017	0.001	0.019
volcano.plot	0.011	0.000	0.011
weight_matrix-methods	0.003	0.001	0.005